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- PDB-7yxb: MHC-II dynamics are maintained in HLA-DR allotypes to ensure cata... -

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Basic information

Entry
Database: PDB / ID: 7yxb
TitleMHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange
Components
  • (HLA class II histocompatibility ...) x 2
  • CLIP peptide
KeywordsIMMUNE SYSTEM / HLA-DR4 / CLIP peptide / MHCII
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / Golgi membrane / lysosomal membrane / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
CITRATE ANION / HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.095 Å
AuthorsRoske, Y. / Abualrous, E.T. / Freund, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange.
Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro- ...Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro-Benito, M. / Hofer, T. / Noe, F. / Freund, C.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen DR beta chain
G: CLIP peptide
H: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,44624
Polymers95,0756
Non-polymers1,37118
Water10,989610
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
G: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,28513
Polymers47,5373
Non-polymers74810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-20 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen DR beta chain
H: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,16111
Polymers47,5373
Non-polymers6248
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-22 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.891, 111.485, 212.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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HLA class II histocompatibility ... , 2 types, 4 molecules ACBD

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 22207.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen DR beta chain / MHC class II antigen


Mass: 23193.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A1V1IGJ9

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Protein/peptide , 1 types, 2 molecules GH

#3: Protein/peptide CLIP peptide


Mass: 2136.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM

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Non-polymers , 3 types, 628 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Ammoniumcitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.09→44.081 Å / Num. obs: 67120 / % possible obs: 99 % / Redundancy: 4.56 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.0159 / Net I/σ(I): 9.69
Reflection shellResolution: 2.09→2.22 Å / Mean I/σ(I) obs: 1.28 / Num. unique obs: 10573 / CC1/2: 0.491 / Rrim(I) all: 0.151

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X5X

4x5x


Resolution: 2.095→44.081 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2099 3.13 %
Rwork0.187 64979 -
obs0.1881 67078 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.91 Å2 / Biso mean: 49.4868 Å2 / Biso min: 19.37 Å2
Refinement stepCycle: final / Resolution: 2.095→44.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6418 0 90 610 7118
Biso mean--72.45 52 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056690
X-RAY DIFFRACTIONf_angle_d0.7419070
X-RAY DIFFRACTIONf_chiral_restr0.05958
X-RAY DIFFRACTIONf_plane_restr0.0051184
X-RAY DIFFRACTIONf_dihedral_angle_d8.5034300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0951-2.14380.33031330.3047414296
2.1438-2.19740.36471390.2931426698
2.1974-2.25680.28841370.2679429499
2.2568-2.32320.26141400.259431099
2.3232-2.39820.2991390.26524313100
2.3982-2.48390.28941400.2442433499
2.4839-2.58340.28031380.2342427599
2.5834-2.70090.25521390.2213429299
2.7009-2.84330.25641410.2095437699
2.8433-3.02140.27931400.19824330100
3.0214-3.25460.20481410.1861435599
3.2546-3.5820.20441410.17314373100
3.582-4.10.18431420.1499438699
4.1-5.16430.14361430.12444425100
5.1643-44.080.22441460.1755450898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.44970.37420.44930.65890.02650.6471-0.01510.1017-0.25910.00550.0631-0.07450.08450.0439-0.060.237-0.01210.03460.1572-0.00830.272324.832214.9817-11.7425
21.80620.88510.15140.93170.00050.7088-0.05830.10370.1718-0.08580.04970.0525-0.0810.03910.00910.21110.01690.01650.14090.030.246317.310629.8071-13.9456
32.3751.63981.32111.69340.41561.8983-0.11220.610.0971-0.15040.16860.0201-0.30870.0761-0.05830.40720.04370.03470.5687-0.01980.232628.943932.2935-39.0667
43.13960.53750.92430.2155-0.49711.8426-0.01750.6504-0.3916-0.10140.1788-0.09230.00850.2087-0.16170.34820.05420.06770.4542-0.14120.350935.691116.947-36.9513
54.0911-0.35920.28145.44892.71861.40860.00960.0765-0.35250.05160.06110.31830.3316-0.2693-0.01450.295-0.05540.03690.23580.04960.37582.66148.5255-11.7444
61.3989-0.72030.23424.0122-0.65022.5847-0.24790.5550.0693-0.49260.6542-0.0013-0.33190.7215-0.31850.5259-0.1622-0.00880.9983-0.12140.320921.167620.8995-58.0693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 181)A1 - 181
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 192)B2 - 192
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 181)C2 - 181
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 193)D3 - 193
5X-RAY DIFFRACTION5(chain 'G' and resid 5 through 19)G5 - 19
6X-RAY DIFFRACTION6(chain 'H' and resid 1 through 19)H1 - 19

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